write.psl: Write PSL file from dataframe or GRanges

Description Usage Arguments Value See Also Examples

View source: R/hiReadsProcessor.R

Description

Given a data frame or GRanges object, the function write a tab deliminated PSL file

Usage

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write.psl(x, filename = "out.psl", header = FALSE,
  includeOtherCols = FALSE)

Arguments

x

data frame or GRanges object with required columns for psl file format.

filename

name for the output PSL file. Default is "out.psl"

header

include PSL header line. Default is FALSE.

includeOtherCols

nclude other non PSL specific columns from x in the output. Default is FALSE.

Value

name of the output PSL file

See Also

read.psl, blatSeqs, read.blast8, read.BAMasPSL, pslToRangedObject

Examples

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data(psl)
pslFile <- tempfile()
write.psl(psl, filename = pslFile)

malnirav/hiReadsProcessor documentation built on Sept. 17, 2017, 10:56 a.m.